Immunoglobulin heavy chain isotype switch recombination is a regulated, irreversible, essential process of DNA deletion which alters genomic structure at the immunoglobulin heavy chain locus, joining a rearranged and expressed variable region to a new downstream constant region, deleting the DNA between. The result of switch recombination is to alter how an immunoglobulin molecule removes antigen without altering its specificity for antigen. Switch recombination is initiated by DNA deamination by the B cell-specific factor, AID, and in subsequent steps ubiquitous factors from distinct repair pathways collaborate to cleave and rejoin chromosomal DNA at the heavy chain locus. We propose to define how AID recognizes its DNA target (Aim 1); to determine the mechanisms of the redundant pathways of DNA cleavage, one dependent on uracile nucleoside glycosylase (UNG; Aim 2), and on dependent on MSH2 (Aim 3); to define the sources of sequence heterogeneity and microhomology at switch junctions (Aim 4); and to study dynamic interactions of repair and recombination factors with transcriptionally activated switch regions in vivo (Aim 5). The results of these experiments will provide new understanding of a critical recombination process, and inform our understanding of how ubiquitous repair factors contribute to the immune response and maintain genomic stability.